DOE Joint Genome Institute

  • About Us
  • Phone Book
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Products
    • Science Highlights
    • Scientists
    ear the town of Rifle, Colorado, lies the primary field site for Phase I of the Subsurface Systems Scientific Focus Area 2.0 (SFA 2.0, sponsored by the DOE Office of Biological and Environmental Research—BER).
    Waiting to Respire
    UC Berkeley and JGI researchers joined forces and data sets to describe bacterial genomes for related (“sibling”) lineages that diverged from the bacterial tree before Cyanobacteria and its contemporaries. The information was then used to predict the metabolic strategies applied by a common ancestor to all five lineages.

    Read more

    Field researchers studying drought responses in Panicum hallii at the UT Austin Brackenridge Field Lab. (David Gilbert)
    A Model System for Perennial Grasses
    The DOE supports research programs for developing methods for converting plant biomass into sustainable fuels for cars and jets. By studying a close relative model species like Panicum hallii, researchers can develop crop improvement techniques that could be applied to the candidate bioenergy feedstock switchgrass.

    Read more

    At high temperature, S. paradoxus cells die in the act of cell division, as seen by the dyads with cell bodies shriveled away from the outer cell wall. (Images by Carly Weiss, courtesy of the Brem Lab)
    Mapping Heat Resistance in Yeasts
    In a proof-of-concept study, researchers demonstrated that a new genetic mapping strategy called RH-Seq can identify genes that promote heat resistance in the yeast Saccharomyces cerevisiae, allowing this species to grow better than its closest relative S. paradoxus at high temperatures.

    Read more

  • Our Projects
    • Search JGI Project List
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    Jorge Rodrigues is interested in the biological causes of methane flux variation in the Amazon rainforest. (Courtesy of Jorge Rodrigues)
    Methane Flux in the Amazon
    Wetlands are the single largest global source of atmospheric methane. This project aims to integrate microbial and tree genetic characteristics to measure and understand methane emissions at the heart of the Amazon rainforest.

    Read more

    Vampirovibrio chlorellavorus in yellow on green host. (Courtesy of Judith Brown)
    Infections and Host-Pathogen Interactions of Chlorella
    The non-photosynthetic, predatory cyanobacterium Vampirovibrio chlorellavorus is a globally important obligate pathogen of Chlorella species/strains, which are of interest as biofuel feedstocks.

    Read more

    Morphological diversity of Sordariales growing in the lab. Pierre Gladieux's proposal explores functional diversity in Neurospora and its relatives. (Pierre Gladieux, INRA Montpellier)
    Insights into Functional Diversity in Neurospora
    This proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi.

    Read more

  • Data & Tools
    • IMG
    • Genome Portal
    • MycoCosm
    • Phytozome
    • GOLD
    Click on the image above or click here (https://youtu.be/iSEEw4Vs_B4) to watch a CRISPR Whiteboard Lesson from the Innovative Genomics Institute, this one focuses on the PAM sequence.
    Mining IMG/M for CRISPR-Associated Proteins
    Researchers report the discovery of miniature CRISPR-associated proteins that can target single-stranded DNA. The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. The sequences were then biochemically characterized by a team led by Jennifer Doudna’s group at UC Berkeley.

    Read more

    The Angelo Coast Range Reserve, from which soil samples were taken, protects thousands of acres of the upper watershed of South Fork of the Eel River (shown here) in Mendocino County. (Akos Kokai via Flickr, CC BY 2.0 https://www.flickr.com/photos/on_earth/17307333828/)
    DAS Tool for Genome Reconstruction from Metagenomes
    Through the JGI’s Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. The work was published in Nature Microbiology.

    Read more

    DOE JGI BOOST logo
    New Software Tools Streamline DNA Sequence Design-and-Build Process
    Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows.

    Read more

  • User Programs
    • Calls for User Proposals
    • Special Programs
    • User Support
    • Submit a Proposal
    Cropped image of switchgrass microcosm showing established root network. (James Moran)
    FY 2019 FICUS EMSL-JGI Projects Selected
    Through the EMSL-JGI FICUS calls, users can combine EMSL’s unique imaging, omics and computational resources with cutting-edge genomics, DNA synthesis and complementary capabilities at JGI. This was the sixth FICUS call between EMSL and JGI since the collaborative science initiative was formed.

    Read more

    Preparing for a Sequence Data Deluge
    The approved CSP 2019 proposals leverage new capabilities and higher throughput in DNA sequencing, synthesis and metabolomics. Additionally, just over half of the accepted proposals come from primary investigators who have never led any previously accepted JGI proposal.

    Read more

    The molecule cyclic di-GMP plays a key role in controlling cellulose production and biofilm formation. To better understand cyclic di-GMP signaling pathways, the team developed the first chemiluminescent biosensor system for cyclic di-GMP and showed that it could be used to assay cyclic di-GMP in bacterial lysates. (Image courtesy of Hammond Lab, UC Berkeley)
    Innovative Technology Improves Our Understanding of Bacterial Cell Signaling
    Cyclic di-GMP (Guanine Monophosphate) is found in nearly all types of bacteria and interacts with cell signaling networks that control many basic cellular functions. To better understand the dynamics of this molecule, researchers developed the first chemiluminescent biosensors for measuring cyclic di-GMP in bacteria through work enabled by the JGI’s Community Science Program (CSP).

    Read more

  • News & Publications
    • News Releases
    • Blog
    • Publications
    • Scientific Posters
    • Newsletter
    • Logos
    • Photos
    One of the heated plots at the Harvard Forest (Jeff Blanchard)
    Hidden Giants in Forest Soils
    In Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by JGI and University of Massachusetts-Amherst researchers. Most of the genomes were uncovered using a "mini-metagenomics" approach that reduced the complexity of the soil microbial communities sequenced and analyzed.

    Read more

    Truffle orchard in Lorraine, France. (Francis Martin)
    Symbiosis a Driver of Truffle Diversity
    Truffles are the fruiting bodies of the ectomycorrhizal (ECM) fungal symbionts residing on host plant roots. In Nature Ecology & Evolution, an international team sought insights into the ECM lifestyle of truffle-forming species. They conducted a comparative analysis of eight Pezizomycete fungi, including four species prized as delicacies.

    Read more

    Blyttiomyces helicus on spruce pollen grain. (Joyce Longcore)
    Expanding Fungal Diversity, One Cell at a Time
    In Nature Microbiology, a team led by JGI researchers has developed a pipeline to generate genomes from single cells of uncultivated fungi. The approach was tested on several uncultivated fungal species representing early diverging fungi.

    Read more

News & Publications
Home › News Releases › The MiSIng Piece Revealed: Classifying microbial species in the genomics era

July 9, 2015

The MiSIng Piece Revealed: Classifying microbial species in the genomics era

Neha Varghese is the first author of the Nucleic Acids Research paper describing the MiSI method for classifying microbial species.

Neha Varghese is the first author of the Nucleic Acids Research paper describing the MiSI method for classifying microbial species.

The rapid explosion in the throughput of DNA sequencing due to new technology platforms is fueling an increase in the number of sequenced microbial genomes and driving much greater availability of these data to the research community. Traditionally, identifying the microorganisms selected for sequencing is often decided on the basis of a single universal marker gene. More recently, however, researchers have noticed that the identity of microbes for which whole-genome information has become available does not always match up with the identity determined by the approaches commonly used prior to the advent of next-generation high-throughput sequencing.

In a study published ahead online July 6, 2015 in Nucleic Acids Research (NAR), a team of researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility and their collaborators developed and evaluated a new method for classifying microbial species that could be supplemented – as needed – by traditional approaches relied on by microbiologists for decades. Study first author Neha Varghese of the DOE JGI says the Microbial Species Identifier (MiSI) method meets a “long standing need for a systematic, scalable, and objective microbial species assignment technique.”

“A fast, genome-sequence based method”

The standard whole-genome approach relies on the small subunit ribosomal RNA gene (16S rRNA); without sequencing, researchers used approaches such as DNA-DNA hybridization, phenotypic information – genotyping, phenotyping, or classifying by the chemical compounds that microbes share – to derive the needed information for microbial classification. The MiSI method developed at the DOE JGI relies primarily on genome sequencing and is a combination of two metrics for determining how closely related two genomes are: genome-wide Average Nucleotide Identity (gANI) and alignment fraction (AF). Computational tool development is a critical element of the DOE JGI 10-Year Strategic Vision, essential to characterizing complex biological and environmental systems in support DOE’s research missions, as well as the Institute’s partnership with the National Energy Research Scientific Computing Center (NERSC).

“Scientists and practitioners of microbiology will much appreciate the robust, extensive, taxonomic organization of the microbial world provided by this fast, genome-sequence based method,” said Jim Tiedje, Director of the Center for Microbial Ecology at Michigan State University. “It provides a more accurate and clear-cut means to identify bacteria.” A DOE JGI collaborator on the Great Prairie Soil Metagenome Grand Challenge project, Tiedje and his former student Kostas Konstantinidis, one of the study’s co-authors, jointly developed the original genome-wide gANI metric modified by the DOE JGI team as a basis for the MiSI method.

The algorithm in the gANI method developed by Tiedje and Konstantinidis used segments sampled over the whole genome and the National Center for Biotechnology Information (NCBI) tool Basic Local Alignment Search Tool (BLAST) for sequence alignment. MiSI speeds up the computations dramatically—by about 10-fold—by using nucleotide sequences of genes and a modified BLAST-based similarity search.

The team implemented the MiSI method over a massive database of more than 13,000 bacterial and archaeal high quality genomes selected from the Integrated Microbial Genomes (IMG) database. These genomes were then classified into clusters represented by cliques or clique-groups where connectivity is determined by genomic similarity (a surrogate for evolutionary distance), and thus, for the first time, allowed researchers to diagram how genomes are related to each other across a large phylogenetic space.

The clique-group comprising of pathogenic Burkholderia mallei and Burkholderia pseudomallei strains highlights the ability of MiSI to capture high similarity as well as subtle differences between closely related genomes. (Figure by Neha Varghese)

The clique-group comprising of pathogenic Burkholderia mallei and Burkholderia pseudomallei strains highlights the ability of MiSI to capture high similarity as well as subtle differences between closely related genomes. (Figure by Neha Varghese)

The completely connected nature of these cliques helped the team identify highly conserved cores of species, while the semi-connect nature of clique groups helped identify species that could be revisited taxonomically. Further, since the clustering is based solely on genomic relatedness, the team was able to use this method to determine if an uncultured organism is either related to an existing species or is a novel candidate species.

“A universal method for species identification”

“The implications of using this method in transforming microbiology cannot be overstated,” said Kyrpides, head of the Prokaryote Super Program and co-corresponding author in this study. “We now have a universal method for species identification across all Archaea and Bacteria that relies on the entire genome rather than a single gene, or a small number of marker genes. When applied to all the sequenced genomes currently available, this method enabled us to observe species evolution in action, manifested through what we call clique groups. Perhaps one of the most dramatic observations we had was that more than half of all the species that had more than one sequenced genome, had at least one genome wrongly named.”

Kyrpides went on to say, “This method is also shedding light on the long debated issue of microbial species. The fact that over 86% of all the microbial species for which more than one genome has been sequenced are grouping into separate cliques, strongly supports the notion of a microbial species, as opposed to the idea of genetic continuum among microbial species, which however was observed for a small number of species, about 5%. It would be very interesting to see how these observations evolve as the numbers of microbial genomes sequenced explode.”

The DOE JGI sequencing pipeline is already using the MiSI method to determine the similarity of newly sequenced genomes to existing reference genomes. MiSI is available for use by the general research community through the IMG system and the data used by the DOE JGI team for this study are publicly available at https://ani.jgi-psf.org.

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Filed Under: News Releases

More topics:

  • News Releases
  • Science Highlights
  • Blog
  • CSP Plans
  • Featured Profiles

Related Content:

Defining Quality Virus Data(sets)

Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)

Hidden Giants in Forest Soils

One of the heated plots at the Harvard Forest (Jeff Blanchard)

Symbiosis a Driver of Truffle Diversity

Truffe noire du Peěrigord (Tuber melanosporum). (Francis Martin)

Probing Interactions Among Molecular Mechanisms, Cellular Processes, and Elemental Cycles

Cropped image of switchgrass microcosm showing established root network. (James Moran)

Spotlighting Differences in Closely-Related Species

Expanding Fungal Diversity, One Cell at a Time

Blyttiomyces helicus on spruce pollen grain. (Joyce Longcore)
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Facebook
  • Flickr
  • Google+
  • Instagram
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2019 The Regents of the University of California